Money matters (I): costs of field and laboratory procedures associated with conventional and marker-assisted maize breeding at CIMMYT

This article presents selected results of a study carried out in Mexico at the International Maize and Wheat Improvement Center (CIMMYT) to compare the cost-effectiveness of conventional and marker-assisted maize breeding. Costs associated with use of conventional and marker-assisted selection (MAS) methods were estimated using a spreadsheet-based budgeting approach. This information was used to compare the cost of using conventional screening and MAS to achieve a well-defined breeding objective—identification of plants carrying a mutant recessive form of the opaque2 gene in maize that is associated with Quality Protein Maize (QPM). In addition to generating empirical cost information that will be of use to CIMMYT research managers, the study produced four important insights. First, for any given breeding project, detailed budget analysis will be needed to determine the cost-effectiveness of MAS relative to conventional selection. Second, direct comparisons of unit costs for MAS methods and conventional selection methods provide useful information for research managers, but factors other than cost are likely to play an important role in driving the choice of screening methods. Third, the choice between MAS and conventional selection may be complicated by the fact that the two are not always direct substitutes. Fourth, when used with empirical data from actual breeding programs, spreadsheet-based budgeting tools can be used by research managers to improve the efficiency of existing protocols and to inform decisions about future technology choices.     

Probability of success of breeding strategies for improving pro-vitamin A content in maize

Biofortification for pro-vitamin A content (pVAC) of modern maize inbreds and hybrids is a feasible way to deal with vitamin A deficiency in rural areas in developing countries. The objective of this study was to evaluate the probability of success of breeding strategies when transferring the high pVAC present in donors to elite modern-adapted lines. For this purpose, a genetic model was built based on previous genetic studies, and different selection schemes including phenotypic selection (PS) and marker-assisted selection (MAS) were simulated and compared. MAS for simultaneously selecting all pVAC genes and a combined scheme for selecting two major pVAC genes by MAS followed by ultra performance liquid chromatography screening for the remaining genetic variation on pVAC were identified as being most effective and cost-efficient. The two schemes have 83.7 and 84.8% probabilities of achieving a predefined breeding target on pVAC and adaptation in one breeding cycle under the current breeding scale. When the breeding scale is increased by making 50% more crosses, the probability values could reach 94.8 and 95.1% for the two schemes. Under fixed resources, larger early generation populations with fewer crosses had similar breeding efficiency to smaller early generation populations with more crosses. Breeding on a larger scale was more efficient both genetically and economically. The approach presented in this study could be used as a general way in quantifying probability of success and comparing different breeding schemes in other breeding programs.     

A comparison of results obtained with two methods for assessing yield stability

Summary A major objective of the CIMMYT Maize Program is to develop open-pollinated varieties of maize (Zea mays L.) that are well adapted to a wide range of environments. To achieve this breeding goal, it is essential that the program use a stability technique that will identify high-yielding, stable genotypes accurately in international trials conducted under different environmental conditions. The objective of this study was to compare a spatial method with a modified conventional regression analysis method to determine the yield stability of 27 CIMMYT maize varieties evaluated at 37 locations. The methods also were compared on the basis of their consistency in assessing the stability of varieties when certain locations were omitted, and when subsets of varieties were analyzed. The varieties found to be stable by the spatial method with all sites included in the analysis were also stable (1) when the lowest and highest yielding sites were excluded from the analyses, and (2) when the varieties were considered, along with others, as a subset of the original group of materials. Stability parameters determined by regression analysis, however, varied for some varieties when (1) extreme sites were excluded, and (2) a subset of entries was considered in isolation. Because the spatial method was more consistent in identifying high-yielding stable varieties, it was considered the more useful of the two methods.     

玉米自交系CML470抗南方锈病基因的定位

南方锈病是我国玉米产区的主要病害,玉米抗病品种的利用是控制其为害的一条最为安全和经济的途径。但是,在我国当前的玉米育种中,所利用的玉米南方锈病基因多来自美国杂交种78599等。为寻找新的南方锈病抗病基因,本研究对CIMMYT自交系CML470的抗性进行了遗传分析。结果发现CML470的抗性由一个显性抗病基因（定名为RppC）控制,该抗病基因被定位于10号染色体短臂端部,位于SSR标记umc1380和umc1291之间,分别与两标记相距3.5 cM和8.8 cM。通过回交,并利用分子标记辅助选择,RppC被转移到了优良自交系昌7-2中。     

Single large-scale marker-assisted selection (SLS-MAS)

This paper presents a new approach for plant improvement that interactively combines the use of DNA markers and conventional breeding. This approach involves selecting plants at early generation with a fixed, favorable genetic background at specific loci, conducting a single large-scale marker-assisted selection (SLS-MAS) while maintaining as much as possible the allelic segregation in the rest of the genome. First, the identification of elite lines presenting high allelic complementarity and being outstanding for traits of interest is required to capture favorable alleles from different parental lines. Second, after identification of the most favorable genomic regions for each selected parental line, those lines are intercrossed to develop segregating populations from which plants homozygous for favorable alleles at target loci are selected. One objective of the scheme is to conduct the marker-assisted selection only once, and it requires the selection of a minimum number of plants to maintain sufficient allelic variability at the unselected loci. Therefore, the selection pressure exerted on the segregating population is quite high and the screening of large populations is required to achieve the objectives of the scheme. No selection is applied outside the target genomic regions, to maintain as much as possible the Mendelian allelic segregation among the selected genotypes. After selection with DNA markers, the genetic diversity at un-selected loci may allow breeders to generate new varieties and hybrids through conventional breeding in response to various local needs. Although the single large-scale MAS scheme described here is oriented toward maize and large-scale breeding programs with substantial resources, the flexibility of this scheme would allow breeding programs to develop options compatible with local resources.     

Best linear unbiased prediction and optimum allocation of test resources in maize breeding with doubled haploids

With best linear unbiased prediction (BLUP), information from genetically related candidates is combined to obtain more precise estimates of genotypic values of test candidates and thereby increase progress from selection. We developed and applied theory and Monte Carlo simulations implementing BLUP in 2 two-stage maize breeding schemes and various selection strategies. Our objectives were to (1) derive analytical solutions of the mixed model equations under two breeding schemes, (2) determine the optimum allocation of test resources with BLUP under different assumptions regarding the variance component ratios for grain yield in maize, (3) compare the progress from selection using BLUP and conventional phenotypic selection based on mean performance solely of the candidates, and (4) analyze the potential of BLUP for further improving the progress from selection. The breeding schemes involved selection for testcross performance either of DH lines at both stages (DHTC) or of S₁ families at the first stage and DH lines at the second stage (S₁TC-DHTC). Our analytical solutions allowed much faster calculations of the optimum allocations and superseded matrix inversions to solve the mixed model equations. Compared to conventional phenotypic selection, the progress from selection was slightly higher with BLUP for both optimization criteria, namely the selection gain and the probability to select the best genotypes. The optimum allocation of test resources in S₁TC-DHTC involved ≥10 test locations at both stages, a low number of crosses (≤6) each with 100–300 S₁ families at the first stage, and 500–1,000 DH lines at the second stage. In breeding scheme DHTC, the optimum number of test candidates at the first stage was 5–10 times larger, whereas the number of test locations at the first stage and the number of test candidates at the second stage were strongly reduced compared to S₁TC-DHTC.     

Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms

Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.     

Congruence between selection on breeding values and farmers' selection criteria in sheep breeding under conventional nucleus breeding schemes

Designing breeding schemes suitable for smallholder livestock production systems in developing regions has hitherto been a challenge. The suggested schemes either do not address farmers' breeding goals (centralized station-based nucleus schemes) or yield slow genetic progress (village-based schemes). A new breeding scheme that integrates the merits of previously suggested schemes has been designed for Menz sheep improvement in Ethiopia. It involves selection based on breeding values in nucleus flocks to produce elite rams, a one-time only provision of improved rams to villagers and a follow-up village-based selection to sustain genetic progress in village flocks. Here, we assessed whether conventional selection of breeding rams based on breeding values for production traits, which is the practice in station-based nucleus flocks, meets farmers' breeding objectives. We also elicited determinants of farmers' ram choice. Low but significant correlations were found between rankings of rams based on farmers' selection criteria, estimated breeding values (EBV) and body weight (BW). Appearance traits (such as color and horn) and meat production traits (BW and linear size traits) significantly determined farmers' breeding ram choice. The results imply that conventional selection criteria based solely on EBV for production traits do not address farmers' trait preferences fully, but only partially. Thus, a two-stage selection procedure involving selection on breeding values in nucleus centers followed by farmers' selection among top- ranking candidate rams is recommended. This approach accommodates farmers' preferences and speeds up genetic progress in village-based selection. The Menz sheep scheme could be applied elsewhere with similar situations to transform conventional station-based nucleus breeding activities into participatory breeding programs.     

Tapping the genetic diversity of landraces in allogamous crops with doubled haploid lines: a case study from European flint maize

Key message

Using landraces for broadening the genetic base of elite maize germplasm is hampered by heterogeneity and high genetic load. Production of DH line libraries can help to overcome these problems.

Abstract

Landraces of maize (Zea mays L.) represent a huge reservoir of genetic diversity largely untapped by breeders. Genetic heterogeneity and a high genetic load hamper their use in hybrid breeding. Production of doubled haploid line libraries (DHL) by the in vivo haploid induction method promises to overcome these problems. To test this hypothesis, we compared the line per se performance of 389 doubled haploid (DH) lines across six DHL produced from European flint landraces with that of four flint founder lines (FFL) and 53 elite flint lines (EFL) for 16 agronomic traits evaluated in four locations. The genotypic variance (\(\sigma _{G}^{2}\)) within DHL was generally much larger than that among DHL and exceeded also \(\sigma _{G}^{2}\) of the EFL. For most traits, the means and \(\sigma _{G}^{2}\) differed considerably among the DHL, resulting in different expected selection gains. Mean grain yield of the EFL was 25 and 62% higher than for the FFL and DHL, respectively, indicating considerable breeding progress in the EFL and a remnant genetic load in the DHL. Usefulness of the best 20% lines was for individual DHL comparable to the EFL and grain yield (GY) in the top lines from both groups was similar. Our results corroborate the tremendous potential of landraces for broadening the narrow genetic base of elite germplasm. To make best use of these “gold reserves”, we propose a multi-stage selection approach with optimal allocation of resources to (1) choose the most promising landraces for DHL production and (2) identify the top DH lines for further breeding.

     

动物遗传标记辅助选择研究及其应用

随着分子数量遗传学及其相关学科的发展,有关动物遗传标记辅助选择方面的研究也在不断深入,且已经在动物遗传改良中有了一些成功应用的示例。就如何综合利用表型、系谱和遗传标记信息进行育种值估计的统计学方法研究方面,目前已基本形成了较为完善的统计学方法。同时,在标记辅助选择相对效率及其影响因素,以及标记辅助选择实施方案的研究上也取得了不少喜人的成果。本文综述了动物遗传标记辅助选择研究的一些进展,并对标记辅助选择在动物遗传改良中应用的有关问题进行了讨论。 Abstract:With the development of molecular and quantitative genetics and its related subjects,it made a great progress on the research about animal genetic marker-assisted selection (MAS).There were also some successful examples on the application of MAS to animal genetic improvement.The statistical method which using phenotypic,pedigree and genetic marker information to predict individual breeding values has already been developed.Many achievements were obtained from the researches,which carried on MAS relative efficiency and its affecting factors and selection schemes.The present paper reviewed some progresses of MAS research and discussed some problems about MAS application to animal breeding.     

The strategy and potential utilization of temperate germplasm for tropical germplasm improvement: a case study of maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

The organization of maize (Zea mays L.) germplasm into genetically divergent heterotic groups is the foundation of a successful hybrid maize breeding program. In this study, 94 CIMMYT maize lines (CMLs) and 54 United States germplasm enhancement of maize (GEM) lines were assembled and characterized using 1,266 single nucleotide polymorphisms (SNPs) with high quality. Based on principal component analysis (PCA), the GEM lines and CMLs were clearly separated. In the GEM lines, there were two groups classified by PCA corresponding to the heterotic groups “stiff stalk” and “non-stiff stalk”. CMLs did not form obvious subgroups by PCA. The allelic frequency of each SNP differed in GEM lines and CMLs. In total, 3.6% alleles (46/1,266) of CMLs are absent in GEM lines and 4.4% alleles (56/1,266) of GEM lines are absent in CMLs. The performance of F1 plants (n = 654) produced by crossing between different groups based on pedigree information was evaluated at the breeding nurseries of two CIMMYT stations. Genomic estimated phenotypic values of plant height and days to anthesis for a testing set of 45 F1 crosses were predicted based on the training data of 600 F1 crosses using a best linear unbiased prediction method. The prediction accuracy benefitted from the adoption of the markers associated with quantitative trait loci for both traits; however, it does not necessarily increase with an increase in marker density. It is suggested that genomic selection combined with association analysis could improve prediction efficiency and reduce cost. For hybrid maize breeding in the tropics, incorporating GEM lines which have unique alleles and clear heterotic patterns into tropically adapted lines could be beneficial for enhancing heterosis in grain yields.     

Evaluation of marker-assisted selection through computer simulation

Computer simulation was used to evaluate responses to marker-assisted selection (MAS) and to compare MAS responses with those typical of phenotypic recurrent selection (PRS) in an allogamous annual crop species such as maize (Zea mays L.). Relative to PRS, MAS produced rapid responses early in the selection process; however, the rate of these responses diminished greatly within three to five cycles. The gains from MAS ranged from 44.7 to 99.5% of the maximum potential, depending on the genetic model considered. Linkage distance between markers and quantitative trait loci (QTLs) was the factor which most limited the responses from MAS. When averaged across all models considered, flanking QTLs within two marker loci produced 38% more gain than did selection based on single markers if markers were loosely-linked to a QTL (20% recombination). Flanking markers were much less advantageous when markers were closely-linked to a QTL (5% recombination), producing an advantage over single markers of only 11%. Markers were most effective in fully exploiting the genetic potential when fewer QTLs controlled the trait. Large QTL numbers exacerbated the problem of marker-QTL recombination by requiring more generations for fixation. In annual crop species, MAS may offer a primary advantage of enabling two selection cycles per year versus the 2 years per cycle required by most PRS schemes for the evaluation of testcross progeny. MAS thus appears to allow very rapid gains for the first 2–3 years of recurrent selection, after which time conventional methods might replace MAS to achieve further responses.Publication number 19, 330 of the Minnesota Agricultural Experiment Station     

Accuracy of genomic selection in European maize elite breeding populations

Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3–4 locations. As for maize up to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds great promise for maize breeding programs.     

分子标记辅助聚合两个棉纤维高强主效QTLs的选择效果

利用长江流域推广品种泗棉3号和优异纤维种质系7235为育种亲本,配置了系统育种和修饰回交聚合育种两套群体。基于来自7235的2个高强纤维主效QTL的分子标记,在上述育种群体中进行了分子标记辅助选择效率研究。高强纤维主效QTLfs1是利用(7235×TM1)F2分离群体,通过集团混合分离法检测到的,它可解释纤维强度表型变异的30%以上。高强纤维主效QTLfs2最初是利用(HS42710×TM1)F2分离群体检测到的,它可解释纤维强度表型变异的12.5%以上。进一步的研究表明,该QTL也位于7235优质系中,但与QTLfs1非等位。2套育种分离群体的2个高强纤维主效QTL的分子标记辅助选择效果表明:QTLfs1在不同环境条件下均稳定表达,它对不同遗传背景的育种群体均有显著的选择效果。尽管QTLfs2的选择效果低于QTLfs1,它在高世代育种群体中也表现较高的选择效率。利用分子标记辅助选择具有一定遗传距离的QTLfs1区间,其纤维强度的选择效率将大大增强。通过分子标记对位于不同连锁群上的2个QTL聚合选择,其中选单株的纤维强度显著提高。研究结果为利用分子标记辅助聚合优质QTL提供了成功实例。     

Within-family marker-assisted selection for aquaculture species

A within-family marker-assisted selection scheme was designed for typical aquaculture breeding schemes, where most traits are recorded on sibs of the candidates. Here, sibs of candidates were tested for the trait and genotyped to establish genetic marker effects on the trait. BLUP breeding values were calculated, including information of the markers (MAS) or not (NONMAS). These breeding values were identical for all family members in the NONMAS schemes, but differed between family members in the MAS schemes, making within-family selection possible. MAS had up to twice the total genetic gain of the corresponding NONMAS scheme. MAS was somewhat less effective when heritability increased from 0.06 to 0.12 or when the frequency of the positive allele was < 0.5. The relative efficiency of MAS was higher for schemes with more candidates, because of larger fullsib family sizes. MAS was also more efficient when male:female mating ratio changed from 1:1 to 1:5 or when the QTL explained more of the total genetic variation. Four instead of two markers linked to the QTL increased genetic gain somewhat. There was no significant difference in polygenic genetic gain between MAS and NONMAS for most schemes. The rates of inbreeding were lower for MAS than NON-MAS schemes, because fewer full-sibs were selected by MAS.     

Patterns of genomic variation in Chinese maize inbred lines and implications for genetic improvement

Key message

Genetic relationships among Chinese maize germplasms reveal historical trends in heterotic patterns from Chinese breeding programs and identify line Dan340 as a potential genome donor for elite inbred line Zheng58.

Abstract

The characterization of the genetic relationships, heterotic patterns and breeding history of lines in maize breeding programs allows breeders to efficiently use maize germplasm for line improvement over time. In this study, 269 temperate inbred lines, most of which have been widely used in Chinese maize breeding programs since the 1970s, were genotyped using the Illumina MaizeSNP50 BeadChip, which contains 56,110 single-nucleotide polymorphisms. The STRUCTURE analysis, cluster analysis and principal coordinate analysis results consistently revealed seven groups, of which five were consistent with known heterotic groups within the Chinese maize germplasm—Domestic Reid, Lancaster, Zi330, Tang SPT and Tem-tropic I (also known as “P”). These genetic relationships also allowed us to determine the historical trends in heterotic patterns during the three decades from 1970 to 2000, represented by Mo17 from Lancaster, HuangZaoSi (HZS) from Tang SPT, Ye478 from Domestic Reid and P178 from Tem-tropic I heterotic groups. Mo17-related commercial hybrids were widely used in the 1970s and 1980s, followed by the release of HZS- and Ye478-related commercial hybrids in the 1980s and 1990s, and the introduction of Tem-tropic I group in the 1990s and 2000s. Additionally, we identified inbred line Dan340 as a potential genome donor for Zheng58, which is the female parent of the most widely grown commercial hybrid ZhengDan958 in China. We also reconstructed the recombination events of elite line HZS and its 14 derived lines. These findings provide useful information to direct future maize breeding efforts.

     

QTL mapping for European corn borer resistance (<Emphasis Type="Italic">Ostrinia nubilalis</Emphasis> Hb.), agronomic and forage quality traits of testcross progenies in early-maturing European maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) germplasm

In hybrid breeding the performance of lines in hybrid combinations is more important than their performance per se. Little information is available on the correlation between individual line and testcross (TC) performances for the resistance to European corn borer (ECB, Ostrinia nubilalis Hb.) in maize (Zea mays L.). Marker assisted selection (MAS) will be successful only if quantitative trait loci (QTL) found in F₂ derived lines for ECB resistance are still expressed in hybrid combinations. The objectives of our study were: (1) to identify and characterize QTL for ECB resistance as well as agronomic and forage quality traits in a population of testcrossed F_2:3 families; (2) to evaluate the consistency of QTL for per se and TC performances; and (3) to determine the association between per se and TC performances of F_2:3 lines for these traits. Two hundred and four F_2:3 lines were derived from the cross between maize lines D06 (resistant) and D408 (susceptible). These lines were crossed to D171 and the TC progenies were evaluated for ECB resistance and agronomic performance in two locations in 2000 and 2001. Using these TC progenies, six QTL for stalk damage rating (SDR) were found. These QTL explained 27.4% of the genotypic variance in a simultaneous fit. Three QTL for SDR were detected consistently for per se and TC performance. Phenotypic and genotypic correlations were low for per se and TC performance for SDR. Correlations between SDR and quality traits were not significant. Based on these results, we conclude that MAS will not be an efficient method for improving SDR. However, new molecular tools might provide the opportunity to use QTL data as a first step to identify genes involved in ECB resistance. Efficient MAS procedures might then be based on markers designed to trace and to combine specific genes and their alleles in elite maize breeding germplasm.Communicated by G. Wenzel     

Evaluation of agronomic traits and analysis of exotic germ plasm polymorphism in adapted x exotic maize crosses

The utilization of exotic germ plasm is difficult due to its non-adaptability. This study investigates the possibility of exotic germ plasm loss during adaptation, and the effect of an additional cross with elite material on the breeding value of exotic x adapted material. The study was conducted on a temperate x highland tropical composite (or pool) developed in order to broaden the genetic variability of maize in north western Europe. The frequency of unique exotic alleles and the isoenzymatic polymorphism at four loci were analysed in the pool itself, in the pool after mild selection, and in the selected pool crossed with elite material. Based on these data, no significant deviation seemed to occur during the mild selection and the cross. The pool and the pool x elite germ plasm cross were evaluated in testcrosses with two complementary testers for both grain and forage production. The pool was later in maturity, more susceptible to lodging, and yielded less than the pool x elite germ plasm crosses for all evaluations. The highest estimates of genetic variance were obtained in the pool for earliness and height traits, and for yield. However, based on the predicted genotypic mean of the selected population, the pool had a lower breeding value than the pool x elite germ plasm cross. The pool x elite germ plasm cross is thus preferred to initiate selection.     

Investigating the efficiency of the single backcrossing breeding strategy through computer simulation

A strategy combining single backcrossing with selected bulk breeding has been successfully used in wheat improvement at CIMMYT to introgress rust resistant genes from donor parents to elite adapted cultivars. In this research, the efficiency of this breeding strategy was compared to other crossing and selection strategies through computer simulation. Results indicated this breeding strategy has advantages in retaining or improving the adaptation of the recurrent parents, and at the same time transferring most of the desired donor genes in a wide range of scenarios. Two rounds of backcrossing have advantages when the adaptation of donor parents is much poorer than that of the adapted parents, but the advantage of three rounds of backcrossing over two rounds is minimal. We recommend using the single backcrossing breeding strategy (SBBS) when three conditions are met: (1) multiple genes govern the phenotypic traits to be transferred from donor parents to adapted parents, (2) the donor parents have some favorable genes that may contribute to the improvement of adaptation in the recipient parents, and (3) conventional phenotypic selection is being applied, or individual genotypes cannot be precisely identified. We envisage that all three conditions commonly exist in modern breeding programs, and therefore believe that SBBS could be applied widely. However, we do not exclude the use of repeated backcrossing if the transferred genes can be precisely identified by closely linked molecular markers, and the donor parents have extremely poor adaptation.     

Impact of selective genotyping in the training population on accuracy and bias of genomic selection

Estimating marker effects based on routinely generated phenotypic data of breeding programs is a cost-effective strategy to implement genomic selection. Truncation selection in breeding populations, however, could have a strong impact on the accuracy to predict genomic breeding values. The main objective of our study was to investigate the influence of phenotypic selection on the accuracy and bias of genomic selection. We used experimental data of 788 testcross progenies from an elite maize breeding program. The testcross progenies were evaluated in unreplicated field trials in ten environments and fingerprinted with 857 SNP markers. Random regression best linear unbiased prediction method was used in combination with fivefold cross-validation based on genotypic sampling. We observed a substantial loss in the accuracy to predict genomic breeding values in unidirectional selected populations. In contrast, estimating marker effects based on bidirectional selected populations led to only a marginal decrease in the prediction accuracy of genomic breeding values. We concluded that bidirectional selection is a valuable approach to efficiently implement genomic selection in applied plant breeding programs.